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Conserved domains on  [gi|1088626142|gb|OHE40403|]
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MAG: hypothetical protein A2013_04950 [Tenericutes bacterium GWE2_38_8]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ferrodoxin_EFR1 super family cl45674
EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight ...
 5-240 1.20e-42

EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight conserved Cys residues in two CxxCxxCxxxCP motifs, each of which binds a 4Fe-4S cluster. The N-terminal region resembles flavodoxin domains, with some members of the family recognized by Pfam models PF12724 (Flavodoxin_5) or PF00258 (Flavodoxin_1).


The actual alignment was detected with superfamily member NF038196:

Pssm-ID: 468407 [Multi-domain]  Cd Length: 243  Bit Score: 146.16  E-value: 1.20e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142   5 IFIFSGTGNTYFIGKKLQDEFKENnvLCDLFTVEKKHDDNrlIDAYDVIGLGYPIYGSDVPLLIRNWIDGLNIQNQKKAF 84
Cdd:NF038196    1 IFYFSGTGNSLYVAKRIAEELGDE--LISISKAIKEGDFK--LKEDEPIGFVFPVYAWGLPRIVEDFIKKLKLKGNKYIF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142  85 VFCTQMMYSGDGAAYGGRLLAKKGFMIRQQAHFNMPNNItdYRILRPFNKHNLIKIEQKKNKQVNRFVKHIltdKKTRKG 164
Cdd:NF038196   77 AVATCGGSIGNALAQLKKLLKKKGLKLSGGFSIKMPNNY--IPLFDVPSKEKAKKILKKAEEKIKEIAEKI---KNRKKG 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088626142 165 SNPISLGLGLFQRIPYQKMEMKWI--SNSIKIEDHCILCKKCIDLCPTGNFEIKDGILKTKNLCFACYRCINHCPVNA 240
Cdd:NF038196  152 PEKKKGFIPRLLSKLVNPLFYKFKvkDKKFHVTDKCIGCGICAKVCPVNNIEMEDGKPVWGHNCTHCLACIHRCPKEA 229
 
Name Accession Description Interval E-value
ferrodoxin_EFR1 NF038196
EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight ...
 5-240 1.20e-42

EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight conserved Cys residues in two CxxCxxCxxxCP motifs, each of which binds a 4Fe-4S cluster. The N-terminal region resembles flavodoxin domains, with some members of the family recognized by Pfam models PF12724 (Flavodoxin_5) or PF00258 (Flavodoxin_1).


Pssm-ID: 468407 [Multi-domain]  Cd Length: 243  Bit Score: 146.16  E-value: 1.20e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142   5 IFIFSGTGNTYFIGKKLQDEFKENnvLCDLFTVEKKHDDNrlIDAYDVIGLGYPIYGSDVPLLIRNWIDGLNIQNQKKAF 84
Cdd:NF038196    1 IFYFSGTGNSLYVAKRIAEELGDE--LISISKAIKEGDFK--LKEDEPIGFVFPVYAWGLPRIVEDFIKKLKLKGNKYIF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142  85 VFCTQMMYSGDGAAYGGRLLAKKGFMIRQQAHFNMPNNItdYRILRPFNKHNLIKIEQKKNKQVNRFVKHIltdKKTRKG 164
Cdd:NF038196   77 AVATCGGSIGNALAQLKKLLKKKGLKLSGGFSIKMPNNY--IPLFDVPSKEKAKKILKKAEEKIKEIAEKI---KNRKKG 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088626142 165 SNPISLGLGLFQRIPYQKMEMKWI--SNSIKIEDHCILCKKCIDLCPTGNFEIKDGILKTKNLCFACYRCINHCPVNA 240
Cdd:NF038196  152 PEKKKGFIPRLLSKLVNPLFYKFKvkDKKFHVTDKCIGCGICAKVCPVNNIEMEDGKPVWGHNCTHCLACIHRCPKEA 229
FldA COG0716
Flavodoxin [Energy production and conversion]; Flavodoxin is part of the Pathway/BioSystem: ...
 3-111 2.02e-18

Flavodoxin [Energy production and conversion]; Flavodoxin is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 440480 [Multi-domain]  Cd Length: 135  Bit Score: 79.18  E-value: 2.02e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142   3 IAIFIFSGTGNTYFIGKKLQDEFKENNVlcDLFTVEKKHDDNrlIDAYDVIGLGYPIYGSDVPLLIRNWIDGL-NIQNQK 81
Cdd:COG0716     1 ILIVYGSTTGNTEKVAEAIAEALGAAGV--DLFEIEDADLDD--LEDYDLLILGTPTWAGELPDDWEDFLEELkEDLSGK 76

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1088626142  82 KAFVFCTqmmysGDGAAYG------GRLLAKKGFMI 111
Cdd:COG0716    77 KVALFGT-----GDSSGYGdalgelKELLEEKGAKV 107
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 192-246 2.73e-06

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 45.85  E-value: 2.73e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088626142 192 IKIEDHCILCKKCIDLCPTGNFEIKDGILKTKNL------CFACYRCINHCPVNALHCSKN 246
Cdd:cd10549     2 KYDPEKCIGCGICVKACPTDAIELGPNGAIARGPeidedkCVFCGACVEVCPTGAIELTPE 62
rnfB TIGR01944
electron transport complex, RnfABCDGE type, B subunit; The six subunit complex RnfABCDGE in ...
 195-241 2.76e-06

electron transport complex, RnfABCDGE type, B subunit; The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit. [Energy metabolism, Electron transport]


Pssm-ID: 273887 [Multi-domain]  Cd Length: 165  Bit Score: 46.33  E-value: 2.76e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1088626142 195 EDHCILCKKCIDLCPTgnfeikDGILKT--------KNLCFACYRCINHCPVNAL 241
Cdd:TIGR01944 112 EDNCIGCTKCIQACPV------DAIVGAakamhtviADECTGCDLCVEPCPTDCI 160
Fer4_7 pfam12838
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 198-240 3.73e-06

4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.


Pssm-ID: 463724 [Multi-domain]  Cd Length: 51  Bit Score: 43.28  E-value: 3.73e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1088626142 198 CILCKKCIDLCPTGNFEI-----KDGILKTK---NLCFACYRCINHCPVNA 240
Cdd:pfam12838   1 CIGCGACVAACPVGAITLdevgeKKGTKTVVidpERCVGCGACVAVCPTGA 51
PRK00783 PRK00783
DNA-directed RNA polymerase subunit D; Provisional
 192-242 4.46e-06

DNA-directed RNA polymerase subunit D; Provisional


Pssm-ID: 234837 [Multi-domain]  Cd Length: 263  Bit Score: 46.80  E-value: 4.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1088626142 192 IKIEDHCILCKKCIDLCPTGNFEIKDGILKTKNL--CFACYRCINHCPVNALH 242
Cdd:PRK00783  165 IEVSEDCDECEKCVEACPRGVLELKEGKLVVTDLlnCSLCKLCERACPGKAIR 217
 
Name Accession Description Interval E-value
ferrodoxin_EFR1 NF038196
EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight ...
 5-240 1.20e-42

EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight conserved Cys residues in two CxxCxxCxxxCP motifs, each of which binds a 4Fe-4S cluster. The N-terminal region resembles flavodoxin domains, with some members of the family recognized by Pfam models PF12724 (Flavodoxin_5) or PF00258 (Flavodoxin_1).


Pssm-ID: 468407 [Multi-domain]  Cd Length: 243  Bit Score: 146.16  E-value: 1.20e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142   5 IFIFSGTGNTYFIGKKLQDEFKENnvLCDLFTVEKKHDDNrlIDAYDVIGLGYPIYGSDVPLLIRNWIDGLNIQNQKKAF 84
Cdd:NF038196    1 IFYFSGTGNSLYVAKRIAEELGDE--LISISKAIKEGDFK--LKEDEPIGFVFPVYAWGLPRIVEDFIKKLKLKGNKYIF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142  85 VFCTQMMYSGDGAAYGGRLLAKKGFMIRQQAHFNMPNNItdYRILRPFNKHNLIKIEQKKNKQVNRFVKHIltdKKTRKG 164
Cdd:NF038196   77 AVATCGGSIGNALAQLKKLLKKKGLKLSGGFSIKMPNNY--IPLFDVPSKEKAKKILKKAEEKIKEIAEKI---KNRKKG 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088626142 165 SNPISLGLGLFQRIPYQKMEMKWI--SNSIKIEDHCILCKKCIDLCPTGNFEIKDGILKTKNLCFACYRCINHCPVNA 240
Cdd:NF038196  152 PEKKKGFIPRLLSKLVNPLFYKFKvkDKKFHVTDKCIGCGICAKVCPVNNIEMEDGKPVWGHNCTHCLACIHRCPKEA 229
FldA COG0716
Flavodoxin [Energy production and conversion]; Flavodoxin is part of the Pathway/BioSystem: ...
 3-111 2.02e-18

Flavodoxin [Energy production and conversion]; Flavodoxin is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 440480 [Multi-domain]  Cd Length: 135  Bit Score: 79.18  E-value: 2.02e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142   3 IAIFIFSGTGNTYFIGKKLQDEFKENNVlcDLFTVEKKHDDNrlIDAYDVIGLGYPIYGSDVPLLIRNWIDGL-NIQNQK 81
Cdd:COG0716     1 ILIVYGSTTGNTEKVAEAIAEALGAAGV--DLFEIEDADLDD--LEDYDLLILGTPTWAGELPDDWEDFLEELkEDLSGK 76

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1088626142  82 KAFVFCTqmmysGDGAAYG------GRLLAKKGFMI 111
Cdd:COG0716    77 KVALFGT-----GDSSGYGdalgelKELLEEKGAKV 107
COG2768 COG2768
Uncharacterized Fe-S cluster protein [Function unknown];
192-242 3.72e-10

Uncharacterized Fe-S cluster protein [Function unknown];


Pssm-ID: 442050 [Multi-domain]  Cd Length: 74  Bit Score: 55.12  E-value: 3.72e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088626142 192 IKIEDHCILCKKCIDLCPTGNFEIKDGILKT-KNLCFACYRCINHCPVNALH 242
Cdd:COG2768     7 YVDEEKCIGCGACVKVCPVGAISIEDGKAVIdPEKCIGCGACIEVCPVGAIK 58
DsrA COG2221
Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion ...
 195-242 2.92e-09

Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion transport and metabolism];


Pssm-ID: 441823 [Multi-domain]  Cd Length: 69  Bit Score: 52.36  E-value: 2.92e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1088626142 195 EDHCILCKKCIDLCPTGNFEIKDGILKTKN-LCFACYRCINHCPVNALH 242
Cdd:COG2221    14 EEKCIGCGLCVAVCPTGAISLDDGKLVIDEeKCIGCGACIRVCPTGAIK 62
NapF COG1145
Ferredoxin [Energy production and conversion];
177-242 7.30e-09

Ferredoxin [Energy production and conversion];


Pssm-ID: 440760 [Multi-domain]  Cd Length: 238  Bit Score: 55.11  E-value: 7.30e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1088626142 177 RIPYQKMEMKWISNSIKIEDHCILCKKCIDLCPTGNFEIKDG---ILKTKNLCFACYRCINHCPVNALH 242
Cdd:COG1145   163 KIEEELKIAIKKAKAVIDAEKCIGCGLCVKVCPTGAIRLKDGkpqIVVDPDKCIGCGACVKVCPVGAIS 231
COG1149 COG1149
MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function ...
 195-242 2.82e-08

MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function prediction only];


Pssm-ID: 440763 [Multi-domain]  Cd Length: 68  Bit Score: 49.73  E-value: 2.82e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1088626142 195 EDHCILCKKCIDLCPTGNFEIKDG--ILKTKNLCFACYRCINHCPVNALH 242
Cdd:COG1149    10 EEKCIGCGLCVEVCPEGAIKLDDGgaPVVDPDLCTGCGACVGVCPTGAIT 59
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 177-240 9.39e-08

TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and conversion];


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 48.50  E-value: 9.39e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1088626142 177 RIPYQKMEMKWISNSIKI-EDHCILCKKCIDLCPTGNFEIKDGILKTK-NLCFACYRCINHCPVNA 240
Cdd:COG4231     2 NITVKILDNRTTAMRYVIdEDKCTGCGACVKVCPADAIEEGDGKAVIDpDLCIGCGSCVQVCPVDA 67
NuoI COG1143
Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy ...
 195-248 8.64e-07

Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]; Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) is part of the Pathway/BioSystem: NADH dehydrogenase


Pssm-ID: 440758 [Multi-domain]  Cd Length: 66  Bit Score: 45.51  E-value: 8.64e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1088626142 195 EDHCILCKKCIDLCPTGNFEIKDGILKTK-----NLCFACYRCINHCPVNALHCSKNAL 248
Cdd:COG1143     1 EDKCIGCGLCVRVCPVDAITIEDGEPGKVyvidpDKCIGCGLCVEVCPTGAISMTPFEL 59
PreA COG1146
NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and ...
 194-241 8.81e-07

NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and metabolism];


Pssm-ID: 440761 [Multi-domain]  Cd Length: 67  Bit Score: 45.47  E-value: 8.81e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088626142 194 IEDHCILCKKCIDLCPTGNFEIKDGILKTKN----LCFACYRCINHCPVNAL 241
Cdd:COG1146     6 DTDKCIGCGACVEVCPVDVLELDEEGKKALVinpeECIGCGACELVCPVGAI 57
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
192-242 9.20e-07

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 49.64  E-value: 9.20e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088626142 192 IKIEDHCILCKKCIDLCPTGNFEIKDGILKTKN-LCFACYRCINHCPVNALH 242
Cdd:COG4624    87 IRDKEKCKNCYPCVRACPVKAIKVDDGKAEIDEeKCISCGQCVAVCPFGAIT 138
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 192-246 2.73e-06

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 45.85  E-value: 2.73e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088626142 192 IKIEDHCILCKKCIDLCPTGNFEIKDGILKTKNL------CFACYRCINHCPVNALHCSKN 246
Cdd:cd10549     2 KYDPEKCIGCGICVKACPTDAIELGPNGAIARGPeidedkCVFCGACVEVCPTGAIELTPE 62
rnfB TIGR01944
electron transport complex, RnfABCDGE type, B subunit; The six subunit complex RnfABCDGE in ...
 195-241 2.76e-06

electron transport complex, RnfABCDGE type, B subunit; The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit. [Energy metabolism, Electron transport]


Pssm-ID: 273887 [Multi-domain]  Cd Length: 165  Bit Score: 46.33  E-value: 2.76e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1088626142 195 EDHCILCKKCIDLCPTgnfeikDGILKT--------KNLCFACYRCINHCPVNAL 241
Cdd:TIGR01944 112 EDNCIGCTKCIQACPV------DAIVGAakamhtviADECTGCDLCVEPCPTDCI 160
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 188-242 2.89e-06

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 45.47  E-value: 2.89e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1088626142 188 ISNSIKIEDHCILCKKCIDLCPTGNFEIKDGILKT----------KNLCFACYRCINHCPVNALH 242
Cdd:cd10549    32 ARGPEIDEDKCVFCGACVEVCPTGAIELTPEGKEYvpkekeaeidEEKCIGCGLCVKVCPVDAIT 96
Fer4_7 pfam12838
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 198-240 3.73e-06

4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.


Pssm-ID: 463724 [Multi-domain]  Cd Length: 51  Bit Score: 43.28  E-value: 3.73e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1088626142 198 CILCKKCIDLCPTGNFEI-----KDGILKTK---NLCFACYRCINHCPVNA 240
Cdd:pfam12838   1 CIGCGACVAACPVGAITLdevgeKKGTKTVVidpERCVGCGACVAVCPTGA 51
PRK00783 PRK00783
DNA-directed RNA polymerase subunit D; Provisional
 192-242 4.46e-06

DNA-directed RNA polymerase subunit D; Provisional


Pssm-ID: 234837 [Multi-domain]  Cd Length: 263  Bit Score: 46.80  E-value: 4.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1088626142 192 IKIEDHCILCKKCIDLCPTGNFEIKDGILKTKNL--CFACYRCINHCPVNALH 242
Cdd:PRK00783  165 IEVSEDCDECEKCVEACPRGVLELKEGKLVVTDLlnCSLCKLCERACPGKAIR 217
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 176-241 8.50e-06

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 44.31  E-value: 8.50e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088626142 176 QRIPYQKMEMKWISNSIKIEDHCILCKKCIDLCPTGNFEIKDGILKT--KNLCFACYRCINHCPVNAL 241
Cdd:cd10549    58 ELTPEGKEYVPKEKEAEIDEEKCIGCGLCVKVCPVDAITLEDELEIVidKEKCIGCGICAEVCPVNAI 125
NapH COG0348
Polyferredoxin NapH [Energy production and conversion];
172-242 1.28e-05

Polyferredoxin NapH [Energy production and conversion];


Pssm-ID: 440117 [Multi-domain]  Cd Length: 263  Bit Score: 45.44  E-value: 1.28e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088626142 172 LGLFQRIPYQKMEMKWISNsikiEDHCILCKKCIDLCPTGNfEIKDGILKTKNlCFACYRCINHCPVNALH 242
Cdd:COG0348   190 YGAFQGLLSDLSTLRVRYD----RGDCIDCGLCVKVCPMGI-DIRKGEINQSE-CINCGRCIDACPKDAIR 254
PRK08348 PRK08348
NADH-plastoquinone oxidoreductase subunit; Provisional
 196-249 2.28e-05

NADH-plastoquinone oxidoreductase subunit; Provisional


Pssm-ID: 181399 [Multi-domain]  Cd Length: 120  Bit Score: 42.90  E-value: 2.28e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1088626142 196 DHCILCKKCIDLCPTGNF----EIKDGILKTKNlCFACYRCINHCPVNALHCSKNALV 249
Cdd:PRK08348   42 DKCVGCRMCVTVCPAGVFvylpEIRKVALWTGR-CVFCGQCVDVCPTGALQMSDDFLL 98
napF TIGR00402
ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of ...
 197-242 2.71e-05

ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation. [Energy metabolism, Electron transport]


Pssm-ID: 273060 [Multi-domain]  Cd Length: 101  Bit Score: 42.24  E-value: 2.71e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1088626142 197 HCILCKKCIDLCPTGNFEIKDGILKTKNL----CFACYRCINHCPVNALH 242
Cdd:TIGR00402  35 VCTRCGECASACENNILQLGQQGQPTVEFdnaeCDFCGKCAEACPTNAFH 84
RNAP_D cd07030
D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is ...
 192-242 2.81e-05

D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.


Pssm-ID: 132908 [Multi-domain]  Cd Length: 259  Bit Score: 44.57  E-value: 2.81e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1088626142 192 IKIEDHCILCKKCIDLCPTGNFEIKDGILKTKNL--CFACYRCINHCPVNALH 242
Cdd:cd07030   165 IEIDEDCDGCGKCVEECPRGVLELEEGKVVVEDLedCSLCKLCERACDAGAIR 217
PRK07118 PRK07118
Fe-S cluster domain-containing protein;
198-250 4.88e-05

Fe-S cluster domain-containing protein;


Pssm-ID: 235941 [Multi-domain]  Cd Length: 280  Bit Score: 43.77  E-value: 4.88e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1088626142 198 CILCKKCIDLCPTGNFEIKDGILKT-KNLCFACYRCINHCPVNALHCSKNALVK 250
Cdd:PRK07118  215 CIGCGKCVKACPAGAITMENNLAVIdQEKCTSCGKCVEKCPTKAIRILNKPPKV 268
PRK09267 PRK09267
flavodoxin FldA; Validated
 1-61 5.05e-05

flavodoxin FldA; Validated


Pssm-ID: 236439 [Multi-domain]  Cd Length: 169  Bit Score: 42.90  E-value: 5.05e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088626142   1 MKIAIFIFSGTGNTYFIGKKLQDEFKENNVlcDLFTVEKKhdDNRLIDAYDVIGLGYPIYG 61
Cdd:PRK09267    2 AKIGIFFGSDTGNTEDIAKMIQKKLGKDVA--DVVDIAKA--SKEDFEAYDLLILGIPTWG 58
PRK06273 PRK06273
ferredoxin; Provisional
 180-241 1.22e-04

ferredoxin; Provisional


Pssm-ID: 235764 [Multi-domain]  Cd Length: 165  Bit Score: 41.62  E-value: 1.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142 180 YQKMEM--KWISNSIK-----IEDHCILCKKCIDLCPTGNFE--------IKDGILKTK------NLCFACYRCINHCPV 238
Cdd:PRK06273   26 YTDKEMrnAILTGTVElpkkvFEELCIGCGGCANVCPTKAIEmipvepvkITEGYVKTKipkidyEKCVYCLYCHDFCPV 105


                  ...
gi 1088626142 239 NAL 241
Cdd:PRK06273  106 FAL 108
DMSOR_beta_like cd16372
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 198-241 4.07e-04

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319894 [Multi-domain]  Cd Length: 125  Bit Score: 39.24  E-value: 4.07e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1088626142 198 CILCKKCIDLCPTGNFEI-KDGILK-TKNLCFACYRCINHCPVNAL 241
Cdd:cd16372    49 CNQCGECIDVCPTGAITRdANGVVMiNKKLCVGCLMCVGFCPEGAM 94
PRK12809 PRK12809
putative oxidoreductase Fe-S binding subunit; Reviewed
 189-241 4.29e-04

putative oxidoreductase Fe-S binding subunit; Reviewed


Pssm-ID: 183762 [Multi-domain]  Cd Length: 639  Bit Score: 41.55  E-value: 4.29e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1088626142 189 SNSIKI-EDHCILCKKCIDLCPTGNFEIKDGILKTKNLC----FACYRCINHCPVNAL 241
Cdd:PRK12809   77 SDSVQLdEQKCIGCKRCAIACPFGVVEMVDTIAQKCDLCnqrsSGTQACIEVCPTQAL 134
HycB COG1142
Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];
194-243 6.46e-04

Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];


Pssm-ID: 440757 [Multi-domain]  Cd Length: 138  Bit Score: 39.26  E-value: 6.46e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1088626142 194 IEDHCILCKKCIDLCPTGNFEIKDGILKTK----NLCFACYR---CINHCPVNALHC 243
Cdd:COG1142    79 DEEKCIGCGLCVLACPFGAITMVGEKSRAVavkcDLCGGREGgpaCVEACPTGALRL 135
PRK06242 PRK06242
flavodoxin; Provisional
 1-111 1.23e-03

flavodoxin; Provisional


Pssm-ID: 180484 [Multi-domain]  Cd Length: 150  Bit Score: 38.36  E-value: 1.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626142   1 MKIAIFIFS-GTGNTYFIGKKLQDEFKennvlCDLFTVEKKHDDNrlIDAYDVIGLGYPIYGSDVPLLIRNWIDGLNIQN 79
Cdd:PRK06242    1 MKALIVYASvHHGNTEKIAKAIAEVLD-----AEVIDPGDVNPED--LSEYDLIGFGSGIYFGKFHKSLLKLIEKLPPVS 73

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1088626142  80 QKKAFVFCTqmmySGDGAAYGGR----LLAKKGFMI 111
Cdd:PRK06242   74 GKKAFIFST----SGLPFLKYHKalkkKLKEKGFEI 105
RnfB COG2878
Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and ...
 187-242 1.53e-03

Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and conversion]; Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase


Pssm-ID: 442125 [Multi-domain]  Cd Length: 254  Bit Score: 39.21  E-value: 1.53e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088626142 187 WISNSIKIEDHCILCKKCIDLCPTgnfeikDGILKTKN--------LCFACYRCINHCPVNALH 242
Cdd:COG2878   128 VIGGPKGCEYGCIGCGDCIKACPF------DAIVGAAKgmhtvdedKCTGCGLCVEACPVDCIE 185
NapF_like cd10564
NapF, iron-sulfur subunit of periplasmic nitrate reductase; This family contains NapF protein, ...
 187-242 1.78e-03

NapF, iron-sulfur subunit of periplasmic nitrate reductase; This family contains NapF protein, the iron-sulfur subunit of periplasmic nitrate reductase. The periplasmic nitrate reductase NapABC of Escherichia coli likely functions during anaerobic growth in low-nitrate environments; napF operon expression is activated by cyclic AMP receptor protein (Crp). NapF is a subfamily of the beta subunit of DMSO reductase (DMSOR) family. DMSOR family members have a large, periplasmic molybdenum-containing alpha subunit as well as a small beta FeS subunit, and may also have a small gamma subunit. The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319886 [Multi-domain]  Cd Length: 139  Bit Score: 37.99  E-value: 1.78e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1088626142 187 WISNSIKIEDHCILCKKCIDLCPTgnfeikdGILK-----------TKNLCFACYRCINHCPVNALH 242
Cdd:cd10564     4 WAVDEALFLDLCTRCGDCVEACPE-------GIIVrgdggfpeldfSRGECTFCGACAEACPEGALD 63
PRK08348 PRK08348
NADH-plastoquinone oxidoreductase subunit; Provisional
 173-220 1.99e-03

NADH-plastoquinone oxidoreductase subunit; Provisional


Pssm-ID: 181399 [Multi-domain]  Cd Length: 120  Bit Score: 37.51  E-value: 1.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1088626142 173 GLFQRIPYQKMEMKWISNsikiedhCILCKKCIDLCPTGNFEIKDGIL 220
Cdd:PRK08348   57 GVFVYLPEIRKVALWTGR-------CVFCGQCVDVCPTGALQMSDDFL 97
PRK05568 PRK05568
flavodoxin; Provisional
 2-64 2.21e-03

flavodoxin; Provisional


Pssm-ID: 235508 [Multi-domain]  Cd Length: 142  Bit Score: 37.48  E-value: 2.21e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088626142   2 KIAIFIFSGTGNTYFIGKKLQDEFKENNVLCDLFTV-EKKHDDnrlIDAYDVIGLGYPIYGSDV 64
Cdd:PRK05568    3 KINIIYWSGTGNTEAMANLIAEGAKENGAEVKLLNVsEASVDD---VKGADVVALGSPAMGDEV 63
PRK05113 PRK05113
electron transport complex protein RnfB; Provisional
 195-239 2.53e-03

electron transport complex protein RnfB; Provisional


Pssm-ID: 235347 [Multi-domain]  Cd Length: 191  Bit Score: 38.00  E-value: 2.53e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1088626142 195 EDHCILCKKCIDLCPTgnfeikDGILKT--------KNLCFACYRCINHCPVN 239
Cdd:PRK05113  113 EDNCIGCTKCIQACPV------DAIVGAtkamhtviSDLCTGCDLCVAPCPTD 159
HdrC COG1150
Heterodisulfide reductase, subunit C [Energy production and conversion];
198-239 3.15e-03

Heterodisulfide reductase, subunit C [Energy production and conversion];


Pssm-ID: 440764 [Multi-domain]  Cd Length: 79  Bit Score: 35.65  E-value: 3.15e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1088626142 198 CILCKKCIDLCPTGNF--------------EIKDGILKTKN--LCFACYRCINHCPVN 239
Cdd:COG1150     5 CYQCGTCTASCPVARAmdynprkiirlaqlGLKEEVLKSDSiwLCVSCYTCTERCPRG 62
QueG COG1600
Epoxyqueuosine reductase QueG (queuosine biosynthesis) [Translation, ribosomal structure and ...
 194-211 3.85e-03

Epoxyqueuosine reductase QueG (queuosine biosynthesis) [Translation, ribosomal structure and biogenesis]; Epoxyqueuosine reductase QueG (queuosine biosynthesis) is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441208 [Multi-domain]  Cd Length: 345  Bit Score: 38.26  E-value: 3.85e-03
                          10
                  ....*....|....*...
gi 1088626142 194 IEDHCILCKKCIDLCPTG 211
Cdd:COG1600   182 VEDHCGSCTRCLDACPTG 199
HdrA COG1148
Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];
195-242 4.13e-03

Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];


Pssm-ID: 440762 [Multi-domain]  Cd Length: 563  Bit Score: 38.30  E-value: 4.13e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1088626142 195 EDHCILCKKCIDLCPTG--NFEIKDGILKTKNLCFACYRCINHCPVNALH 242
Cdd:COG1148   495 PEKCTGCGRCVEVCPYGaiSIDEKGVAEVNPALCKGCGTCAAACPSGAIS 544
PhsB_like cd10553
uncharacterized beta subfamily of DMSO Reductase similar to Desulfonauticus sp PhsB; This ...
 168-237 6.04e-03

uncharacterized beta subfamily of DMSO Reductase similar to Desulfonauticus sp PhsB; This family includes beta FeS subunits of anaerobic DMSO reductase (DMSOR) superfamily that have yet to be characterized. DMSOR consists of a large, periplasmic molybdenum-containing alpha subunit as well as a small beta FeS subunit, and may also have a small gamma subunit. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and the tungsten-containing formate dehydrogenase (FDH-T). Examples of heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319875 [Multi-domain]  Cd Length: 146  Bit Score: 36.57  E-value: 6.04e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1088626142 168 ISLGLGLFQRIPyqKMEMKWISnsikiedhCILCKK--CIDLCPTGNFE--IKDGILKTK-NLCFACYRCINHCP 237
Cdd:cd10553    38 FAVGPKMVGGKP--RLKFVYMS--------CFHCENpwCVKACPTGAMQkrEKDGIVYVDqELCIGCKACIEACP 102
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
188-242 9.09e-03

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 37.31  E-value: 9.09e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1088626142 188 ISNSIKIEDHCILCKKCIDLCPTGNFEIKDGILK-------TKNLCFACYRCINHCPVNALH 242
Cdd:COG4624    48 CSCCPRCCLCCCCCCRCCVAISCIQVRGIIIIDKrgpsiirDKEKCKNCYPCVRACPVKAIK 109
PRK13795 PRK13795
hypothetical protein; Provisional
 198-238 9.23e-03

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 37.28  E-value: 9.23e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1088626142 198 CILCKKCIDLCPTGNFEIKDGILKTKNL---CFACYRCINHCPV 238
Cdd:PRK13795  583 CVGCGVCVGACPTGAIRIEEGKRKISVDeekCIHCGKCTEVCPV 626
Fer4_10 pfam13237
4Fe-4S dicluster domain; This family includes proteins containing domains which bind to ...
 192-237 9.61e-03

4Fe-4S dicluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.


Pssm-ID: 404174 [Multi-domain]  Cd Length: 56  Bit Score: 33.76  E-value: 9.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1088626142 192 IKIEDHCILCKKCIDLCPTGNF------EIKDGILKTKNL--CFACYRCINHCP 237
Cdd:pfam13237   3 VIDPDKCIGCGRCTAACPAGLTrvgaivERLEGEAVRIGVwkCIGCGACVEACP 56
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
194-225 9.67e-03

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 37.31  E-value: 9.67e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1088626142 194 IEDHCILCKKCIDLCPTGNFEIKDGILKTKNL 225
Cdd:COG4624   118 DEEKCISCGQCVAVCPFGAITEKSDIEKVKKA 149
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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